Merge remote-tracking branch 'zprince/component_flux_up' into drewj/b…

…u-rotate-with-pin-dep

* zprince/component_flux_up:
  fix linting
  release notes
  Enabling axial expansion with detailed depletion (#1954)
  Improving error testing (#2004)
  Addressing reviewer comments for component pin mg fluxes
  Removing mystery coverage line from tests (#2003)
  beef up assertions
  resolve fixme
  org imports
  No need to recast strings to strings
  Finishing up the numProcessors -> nTasks conversion (#2002)
  Using one-block reactor for component flux test
  Supporting Python 3.13 (#1996)
  Removing SmartList & adding coverage (#1992)
  Update `copyOrWarn` and `getFileSHA1Hash` to account for directories (#1984)
  Removing broken plot (#1994)
  Adding unit tests for `CylindricalComponentsDuctHetAverageBlockCollection` (#1991)
  Allowing creation of partially heterogeneous assemblies for 1D XS model (#1949)

.github/workflows/coverage.yaml

@@ -44,6 +44,7 @@ jobs:
           mpiexec -n 2 --use-hwthread-cpus coverage run --rcfile=pyproject.toml -m pytest --cov=armi --cov-config=pyproject.toml --cov-report=lcov --cov-append --ignore=venv armi/tests/test_mpiParameters.py || true
           mpiexec -n 2 --use-hwthread-cpus coverage run --rcfile=pyproject.toml -m pytest --cov=armi --cov-config=pyproject.toml --cov-report=lcov --cov-append --ignore=venv armi/tests/test_mpiDirectoryChangers.py || true
           coverage combine --rcfile=pyproject.toml --keep -a
+          coverage report --rcfile=pyproject.toml -i --skip-empty --skip-covered --sort=cover --fail-under=90
       - name: Publish to coveralls.io
         uses: coverallsapp/github-action@v2
         with:

.github/workflows/unittests.yaml

@@ -21,14 +21,15 @@ jobs:
     runs-on: ubuntu-24.04
     strategy:
       matrix:
-        python: [3.9, '3.10', '3.11', '3.12']
+        python: [3.9, '3.10', '3.11', '3.12', '3.13']
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Setup Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python }}
+          allow-prereleases: true
       - name: Update package index
         run: sudo apt-get update
       - name: Install mpi libs
@@ -37,6 +38,6 @@ jobs:
         run: |
           pip install -e .[memprof,mpi,test]
           pytest -n 4 armi
-          mpiexec -n 2 --use-hwthread-cpus coverage run --rcfile=pyproject.toml -m pytest --cov=armi --cov-config=pyproject.toml --ignore=venv armi/tests/test_mpiFeatures.py || true
-          mpiexec -n 2 --use-hwthread-cpus coverage run --rcfile=pyproject.toml -m pytest --cov=armi --cov-config=pyproject.toml --ignore=venv armi/tests/test_mpiParameters.py || true
-          mpiexec -n 2 --use-hwthread-cpus coverage run --rcfile=pyproject.toml -m pytest --cov=armi --cov-config=pyproject.toml --ignore=venv armi/utils/tests/test_directoryChangersMpi.py || true
+          mpiexec -n 2 --use-hwthread-cpus pytest armi/tests/test_mpiFeatures.py
+          mpiexec -n 2 --use-hwthread-cpus pytest armi/tests/test_mpiParameters.py
+          mpiexec -n 2 --use-hwthread-cpus pytest armi/utils/tests/test_directoryChangersMpi.py

armi/bookkeeping/db/tests/test_comparedb3.py

@@ -228,15 +228,17 @@ def test_diffSpecialData(self):
             refData4 = f4.create_dataset("numberDensities", data=a2)
             refData4.attrs["shapes"] = "2"
             refData4.attrs["numDens"] = a2
+            refData4.attrs["specialFormatting"] = True
             f5 = h5py.File("test_diffSpecialData5.hdf5", "w")
             srcData5 = f5.create_dataset("numberDensities", data=a2)
             srcData5.attrs["shapes"] = "2"
             srcData5.attrs["numDens"] = a2
+            srcData5.attrs["specialFormatting"] = True
 
-            # there should an exception
-            with self.assertRaises(Exception) as e:
+            # there should a log message
+            with mockRunLogs.BufferLog() as mock:
                 _diffSpecialData(refData4, srcData5, out, dr)
-                self.assertIn("Unable to unpack special data for paramName", e)
+                self.assertIn("Unable to unpack special data for", mock.getStdout())
 
             # make an H5 datasets that will add a np.inf diff because keys don't match
             f6 = h5py.File("test_diffSpecialData6.hdf5", "w")

armi/cases/case.py

@@ -855,7 +855,7 @@ def _copyInputsHelper(
     -------
     destFilePath (or origFile) : str
     """
-    sourceName = os.path.basename(sourcePath)
+    sourceName = pathlib.Path(sourcePath).name
     destFilePath = os.path.join(destPath, sourceName)
     try:
         pathTools.copyOrWarn(fileDescription, sourcePath, destFilePath)
@@ -880,9 +880,10 @@ def copyInterfaceInputs(
     This function should now be able to handle the updating of:
 
       - a single file (relative or absolute)
-      - a list of files (relative or absolute), and
+      - a list of files (relative or absolute)
       - a file entry that has a wildcard processing into multiple files.
         Glob is used to offer support for wildcards.
+      - a directory and its contents
 
     If the file paths are absolute, do nothing. The case will be able to find the file.
 
@@ -950,7 +951,7 @@ def copyInterfaceInputs(
                 path = pathlib.Path(f)
                 if not WILDCARD and not RELATIVE:
                     try:
-                        if path.is_absolute() and path.exists() and path.is_file():
+                        if path.is_absolute() and path.exists():
                             # Path is absolute, no settings modification or filecopy needed
                             newFiles.append(path)
                             continue

armi/nuclearDataIO/nuclearFileMetadata.py

@@ -252,4 +252,4 @@ def _getSkippedKeys(self, other, selfContainer, otherContainer, mergedData):
 
 
 class NuclideMetadata(_Metadata):
-    """Simple dictionary for providing metadata about how to read/write a nuclde to/from a file."""
+    """Simple dictionary for providing metadata about how to read/write a nuclide to/from a file."""

armi/nuclearDataIO/tests/test_xsLibraries.py

@@ -127,7 +127,7 @@ def test_mergeFailsWithNonIsotxsFiles(self):
             os.remove(dummyFileName)
 
         with TemporaryDirectoryChanger():
-            dummyFileName = "ISOtopics.txt"
+            dummyFileName = "ISO[]"
             with open(dummyFileName, "w") as file:
                 file.write(
                     "This is a file that starts with the letters 'ISO' but will"

armi/nuclearDataIO/xsLibraries.py

@@ -127,7 +127,7 @@ def getISOTXSLibrariesToMerge(xsLibrarySuffix, xsLibFileNames):
         isosWithSuffix = [
             iso
             for iso in isosToMerge
-            if re.match(f".*ISO[A-Z]{{2}}F?{xsLibrarySuffix}$", iso)
+            if re.match(f".*ISO[A-Za-z]{{2}}F?{xsLibrarySuffix}$", iso)
         ]
         isosToMerge = [
             iso
@@ -193,7 +193,7 @@ def mergeXSLibrariesInWorkingDirectory(
     for xsLibFilePath in sorted(xsLibFiles):
         try:
             # get XS ID from the cross section library name
-            xsID = re.search("ISO([A-Z0-9]{2})", xsLibFilePath).group(1)
+            xsID = re.search("ISO([A-Z0-9a-z]{2})", xsLibFilePath).group(1)
         except AttributeError:
             # if glob has matched something that is not actually an ISOXX file,
             # the .group() call will fail

armi/physics/neutronics/crossSectionGroupManager.py

@@ -63,6 +63,7 @@
 from armi.physics.neutronics.const import CONF_CROSS_SECTION
 from armi.reactor import flags
 from armi.reactor.components import basicShapes
+from armi.reactor.converters.blockConverters import stripComponents
 from armi.reactor.flags import Flags
 from armi.utils.units import TRACE_NUMBER_DENSITY
 
@@ -623,7 +624,11 @@ def _getAverageComponentNucs(self, components, bWeights):
             weight = bWeight * c.getArea()
             totalWeight += weight
             densities += weight * np.array(c.getNuclideNumberDensities(allNucNames))
-        return allNucNames, densities / totalWeight
+        if totalWeight > 0.0:
+            weightedDensities = densities / totalWeight
+        else:
+            weightedDensities = np.zeros_like(densities)
+        return allNucNames, weightedDensities
 
     def _orderComponentsInGroup(self, repBlock):
         """Order the components based on dimension and material type within the representative
@@ -648,6 +653,64 @@ def _getNucTempHelper(self):
         return nvt, nv
 
 
+class CylindricalComponentsDuctHetAverageBlockCollection(
+    CylindricalComponentsAverageBlockCollection
+):
+    """
+    Creates a representative block for the purpose of cross section generation with a one-
+    dimensional cylindrical model where all material inside the duct is homogenized.
+
+    .. impl:: Create partially heterogeneous representative blocks.
+        :id: I_ARMI_XSGM_CREATE_REPR_BLOCKS2
+        :implements: R_ARMI_XSGM_CREATE_REPR_BLOCKS
+
+        This class constructs representative blocks based on a volume-weighted average using
+        cylindrical blocks from an existing block list. Inheriting functionality from the abstract
+        :py:class:`Reactor <armi.physics.neutronics.crossSectionGroupManager.BlockCollection>`
+        object, this class will construct representative blocks using averaged parameters of all
+        blocks in the given collection. Number density averages are computed at a component level.
+        Nuclide temperatures from a median block-average temperature are used and the average burnup
+        is evaluated across all blocks in the block list.
+
+        The average nuclide temperatures are calculated only for the homogenized region inside of
+        the duct. For the non-homogenized regions, the MC2 writer uses the component temperatures.
+
+    Notes
+    -----
+    The representative block for this collection is the same as the parent. The only difference between
+    the two collection types is that this collection calculates average nuclide temperatures based only
+    on the components that are inside of the duct.
+    """
+
+    def _getNewBlock(self):
+        newBlock = copy.deepcopy(self._selectCandidateBlock())
+        newBlock.name = "1D_CYL_DUCT_HET_AVG_" + newBlock.getMicroSuffix()
+        return newBlock
+
+    def _makeRepresentativeBlock(self):
+        """Build a representative fuel block based on component number densities."""
+        self.calcAvgNuclideTemperatures()
+        return CylindricalComponentsAverageBlockCollection._makeRepresentativeBlock(
+            self
+        )
+
+    def _getNucTempHelper(self):
+        """All candidate blocks are used in the average."""
+        nvt = np.zeros(len(self.allNuclidesInProblem))
+        nv = np.zeros(len(self.allNuclidesInProblem))
+        for block in self.getCandidateBlocks():
+            wt = self.getWeight(block)
+            # remove the duct and intercoolant from the block before
+            # calculating average nuclide temps
+            newBlock, _mixtureFlags = stripComponents(block, Flags.DUCT)
+            nvtBlock, nvBlock = getBlockNuclideTemperatureAvgTerms(
+                newBlock, self.allNuclidesInProblem
+            )
+            nvt += nvtBlock * wt
+            nv += nvBlock * wt
+        return nvt, nv
+
+
 class SlabComponentsAverageBlockCollection(BlockCollection):
     """
     Creates a representative 1D slab block.
@@ -789,7 +852,11 @@ def _getAverageComponentNucs(self, components, bWeights):
             weight = bWeight * c.getArea()
             totalWeight += weight
             densities += weight * np.array(c.getNuclideNumberDensities(allNucNames))
-        return allNucNames, densities / totalWeight
+        if totalWeight > 0.0:
+            weightedDensities = densities / totalWeight
+        else:
+            weightedDensities = np.zeros_like(densities)
+        return allNucNames, weightedDensities
 
     def _orderComponentsInGroup(self, repBlock):
         """Order the components based on dimension and material type within the representative block."""
@@ -1520,6 +1587,9 @@ def updateNuclideTemperatures(self, blockCollectionByXsGroup=None):
 FLUX_WEIGHTED_AVERAGE_BLOCK_COLLECTION = "FluxWeightedAverage"
 SLAB_COMPONENTS_BLOCK_COLLECTION = "ComponentAverage1DSlab"
 CYLINDRICAL_COMPONENTS_BLOCK_COLLECTION = "ComponentAverage1DCylinder"
+CYLINDRICAL_COMPONENTS_DUCT_HET_BLOCK_COLLECTION = (
+    "ComponentAverage1DCylinderDuctHeterogeneous"
+)
 
 # Mapping between block collection string constants and their
 # respective block collection classes.
@@ -1529,12 +1599,17 @@ def updateNuclideTemperatures(self, blockCollectionByXsGroup=None):
     FLUX_WEIGHTED_AVERAGE_BLOCK_COLLECTION: FluxWeightedAverageBlockCollection,
     SLAB_COMPONENTS_BLOCK_COLLECTION: SlabComponentsAverageBlockCollection,
     CYLINDRICAL_COMPONENTS_BLOCK_COLLECTION: CylindricalComponentsAverageBlockCollection,
+    CYLINDRICAL_COMPONENTS_DUCT_HET_BLOCK_COLLECTION: CylindricalComponentsDuctHetAverageBlockCollection,
 }
 
 
 def blockCollectionFactory(xsSettings, allNuclidesInProblem):
     """Build a block collection based on user settings and input."""
     blockRepresentation = xsSettings.blockRepresentation
+    if (
+        blockRepresentation == CYLINDRICAL_COMPONENTS_BLOCK_COLLECTION
+    ) and xsSettings.ductHeterogeneous:
+        blockRepresentation = CYLINDRICAL_COMPONENTS_DUCT_HET_BLOCK_COLLECTION
     validBlockTypes = xsSettings.validBlockTypes
     averageByComponent = xsSettings.averageByComponent
     return BLOCK_COLLECTIONS[blockRepresentation](

armi/physics/neutronics/crossSectionSettings.py

@@ -49,6 +49,7 @@
 CONF_HOMOGBLOCK = "useHomogenizedBlockComposition"
 CONF_INTERNAL_RINGS = "numInternalRings"
 CONF_MERGE_INTO_CLAD = "mergeIntoClad"
+CONF_MERGE_INTO_FUEL = "mergeIntoFuel"
 CONF_MESH_PER_CM = "meshSubdivisionsPerCm"
 CONF_REACTION_DRIVER = "nuclideReactionDriver"
 CONF_XSID = "xsID"
@@ -57,6 +58,8 @@
 CONF_COMPONENT_AVERAGING = "averageByComponent"
 CONF_XS_MAX_ATOM_NUMBER = "xsMaxAtomNumber"
 CONF_MIN_DRIVER_DENSITY = "minDriverDensity"
+CONF_DUCT_HETEROGENEOUS = "ductHeterogeneous"
+CONF_TRACE_ISOTOPE_THRESHOLD = "traceIsotopeThreshold"
 
 
 class XSGeometryTypes(Enum):
@@ -136,6 +139,7 @@ def getStr(cls, typeSpec: Enum):
         CONF_XSID,
         CONF_GEOM,
         CONF_MERGE_INTO_CLAD,
+        CONF_MERGE_INTO_FUEL,
         CONF_DRIVER,
         CONF_HOMOGBLOCK,
         CONF_INTERNAL_RINGS,
@@ -149,6 +153,8 @@ def getStr(cls, typeSpec: Enum):
         CONF_XS_PRIORITY,
         CONF_XS_MAX_ATOM_NUMBER,
         CONF_MIN_DRIVER_DENSITY,
+        CONF_DUCT_HETEROGENEOUS,
+        CONF_TRACE_ISOTOPE_THRESHOLD,
     },
     XSGeometryTypes.getStr(XSGeometryTypes.TWO_DIMENSIONAL_HEX): {
         CONF_XSID,
@@ -186,6 +192,7 @@ def getStr(cls, typeSpec: Enum):
         vol.Optional(CONF_INTERNAL_RINGS): vol.Coerce(int),
         vol.Optional(CONF_EXTERNAL_RINGS): vol.Coerce(int),
         vol.Optional(CONF_MERGE_INTO_CLAD): [str],
+        vol.Optional(CONF_MERGE_INTO_FUEL): [str],
         vol.Optional(CONF_XS_FILE_LOCATION): [str],
         vol.Optional(CONF_EXTERNAL_FLUX_FILE_LOCATION): str,
         vol.Optional(CONF_MESH_PER_CM): vol.Coerce(float),
@@ -194,6 +201,8 @@ def getStr(cls, typeSpec: Enum):
         vol.Optional(CONF_XS_MAX_ATOM_NUMBER): vol.Coerce(int),
         vol.Optional(CONF_MIN_DRIVER_DENSITY): vol.Coerce(float),
         vol.Optional(CONF_COMPONENT_AVERAGING): bool,
+        vol.Optional(CONF_DUCT_HETEROGENEOUS): bool,
+        vol.Optional(CONF_TRACE_ISOTOPE_THRESHOLD): vol.Coerce(float),
     }
 )
 
@@ -410,6 +419,12 @@ class XSModelingOptions:
         and is sometimes used to merge a "gap" or low-density region into
         a "clad" region to avoid numerical issues.
 
+    mergeIntoFuel : list of str
+        This is a lattice physics configuration option that is a list of component
+        names to merge into a "fuel" component. This is highly-design specific
+        and is sometimes used to merge a "gap" or low-density region into
+        a "fuel" region to avoid numerical issues.
+
     meshSubdivisionsPerCm : float
         This is a lattice physics configuration option that can be used to control
         subregion meshing of the representative block in 1D problems.
@@ -419,7 +434,7 @@ class XSModelingOptions:
         no others will allocate to it. This is useful for time balancing when you
         have one task that takes much longer than the others.
 
-    xsPriority:
+    xsPriority: int
         The priority of the mpi tasks that results from this xsID. Lower priority
         will execute first. starting longer jobs first is generally more efficient.
 
@@ -429,10 +444,31 @@ class XSModelingOptions:
         (e.g., fission products) as a depletion product of an isotope with a much
         smaller atomic number.
 
+    averageByComponent: bool
+        Controls whether the representative block averaging is performed on a
+        component-by-component basis or on the block as a whole. If True, the
+        resulting representative block will have component compositions that
+        largely reflect those of the underlying blocks in the collection. If
+        False, the number densities of some nuclides in the individual
+        components may not be reflective of those of the underlying components
+        due to the block number density "dehomogenization".
+
     minDriverDensity: float
         The minimum number density for nuclides included in driver material for a 1D
         lattice physics model.
 
+    ductHeterogeneous : bool
+        This is a lattice physics configuration option used to enable a partially
+        heterogeneous approximation for a 1D cylindrical model. Everything inside of the
+        duct will be treated as homogeneous.
+
+    traceIsotopeThreshold : float
+        This is a lattice physics configuration option used to enable a separate 0D fuel
+        cross section calculation for trace fission products when using a 1D cross section
+        model. This can significantly reduce the memory and run time required for the 1D
+        model. The setting takes a float value that represents the number density cutoff
+        for isotopes to be considered "trace". If no value is provided, the default is 0.0.
+
     Notes
     -----
     Not all default attributes may be useful for your specific application and you may
@@ -458,12 +494,15 @@ def __init__(
         numInternalRings=None,
         numExternalRings=None,
         mergeIntoClad=None,
+        mergeIntoFuel=None,
         meshSubdivisionsPerCm=None,
         xsExecuteExclusive=None,
         xsPriority=None,
         xsMaxAtomNumber=None,
         averageByComponent=False,
         minDriverDensity=0.0,
+        ductHeterogeneous=False,
+        traceIsotopeThreshold=0.0,
     ):
         self.xsID = xsID
         self.geometry = geometry
@@ -482,10 +521,13 @@ def __init__(
         self.numInternalRings = numInternalRings
         self.numExternalRings = numExternalRings
         self.mergeIntoClad = mergeIntoClad
+        self.mergeIntoFuel = mergeIntoFuel
         self.meshSubdivisionsPerCm = meshSubdivisionsPerCm
         self.xsMaxAtomNumber = xsMaxAtomNumber
         self.minDriverDensity = minDriverDensity
         self.averageByComponent = averageByComponent
+        self.ductHeterogeneous = ductHeterogeneous
+        self.traceIsotopeThreshold = traceIsotopeThreshold
         # these are related to execution
         self.xsExecuteExclusive = xsExecuteExclusive
         self.xsPriority = xsPriority
@@ -668,12 +710,15 @@ def setDefaults(self, blockRepresentation, validBlockTypes):
                 CONF_GEOM: self.geometry,
                 CONF_DRIVER: "",
                 CONF_MERGE_INTO_CLAD: ["gap"],
+                CONF_MERGE_INTO_FUEL: [],
                 CONF_MESH_PER_CM: 1.0,
                 CONF_INTERNAL_RINGS: 0,
                 CONF_EXTERNAL_RINGS: 1,
                 CONF_HOMOGBLOCK: False,
                 CONF_BLOCK_REPRESENTATION: crossSectionGroupManager.CYLINDRICAL_COMPONENTS_BLOCK_COLLECTION,
                 CONF_BLOCKTYPES: validBlockTypes,
+                CONF_DUCT_HETEROGENEOUS: False,
+                CONF_TRACE_ISOTOPE_THRESHOLD: 0.0,
             }
         elif self.geometry == XSGeometryTypes.getStr(
             XSGeometryTypes.TWO_DIMENSIONAL_HEX